pyemaps 2.0.0__py3-none-any.whl

pyemaps/xtal.py

@@ -0,0 +1,222 @@
+'''
+
+.. This file is part of pyEMAPS
+ 
+.. ----
+
+.. pyEMAPS is free software. You can redistribute it and/or modify 
+.. it under the terms of the GNU General Public License as published 
+.. by the Free Software Foundation, either version 3 of the License, 
+.. or (at your option) any later version..
+
+.. pyEMAPS is distributed in the hope that it will be useful,
+.. but WITHOUT ANY WARRANTY; without even the implied warranty of
+.. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+.. GNU General Public License for more details.
+
+.. You should have received a copy of the GNU General Public License
+.. along with pyEMAPS.  If not, see `<https://www.gnu.org/licenses/>`_.
+
+.. Contact supprort@emlabsoftware.com for any questions and comments.
+
+.. ----
+
+.. Author:     EMLab Solutions, Inc.
+.. Date:       Feb. 17, 2025    
+
+'''
+
+from . import MxtalError
+import numpy as np
+
+class ACoord:
+
+    '''
+
+    Coordinates of an atom with its symbol and 3-d real number coordinates in a crystal structure.
+    
+    '''
+    def __init__(self, symb = "", coord=[0.0, 0.0, 0.0]):
+
+        setattr(self, 'symb', symb)
+        setattr(self, 'coord', coord)
+
+    @property
+    def symb(self):
+
+        '''
+
+        atom symbol
+
+        '''
+        return self._symb
+    
+    @property
+    def coord(self):
+
+        '''
+
+        Atom coordinate in 3-d floating numbers
+
+        '''
+        return self._coord
+
+    @symb.setter
+    def symb(self, s):
+        if s is None or not isinstance(s, str):
+            raise MxtalError("Atomic symbol must be a string")
+        self._symb=s
+
+    @coord.setter
+    def coord(self, v):
+        
+        if v is None or not isinstance(v, (list, np.ndarray)) or len(v) != 3 or not all(isinstance(x, (int, float)) for x in v):
+            raise MxtalError("Atomic coordinates must be an array of three float or integer numerals")
+        self._coord=v
+    
+    def __eq__(self, other):
+        import numpy as np
+        if not isinstance(other, ACoord):
+            print(f'Comparing object must of type ACoord')
+            return False
+        
+        if self._symb != other.symb:
+            return False
+        
+        if not np.allclose(self._coord, other.coord, atol=1.0e-6):
+            return False
+
+        return True
+
+    def __repr__(self):
+        s, x, y, z = self._symb, self._coord[0], self._coord[1], self._coord[2]
+        sx = '{0:<#014.10f}'. format(x)
+        sy = '{0:<#014.10f}'. format(y)
+        sz = '{0:<#014.10f}'. format(z)
+        return str(f'{s:<10}\t{sx} {sy} {sz}')
+    
+    def __str__(self):
+        return self.__repr__()
+    
+class Xtal:
+
+    '''
+    Crystal structure class cnostructed by the output from
+    `generateMxtal <pyemaps.crystals.html#pyemaps.crystals.Crystal.generateMxtal>`_ method of any crystal object, which consists of a cell
+    constant and a list of atomic coordinates.
+
+    '''
+    def __init__(self):
+        
+        setattr(self, 'cell', [0.0,0.0,0.0,90.0,90.0,90.0])
+        setattr(self, 'acoordList', [])
+
+    @property
+    def cell(self):
+        return self._cell
+
+    @property
+    def acoordList(self):
+        return self._acoordList
+
+    @cell.setter
+    def cell(self, c):
+        if c is None or not isinstance(c, (list, np.ndarray)) or len(c) != 6 or not all(isinstance(x, (int, float)) for x in c):  
+            raise MxtalError('Invalid cell constants, it much be an array of six floats')
+
+        self._cell = c
+
+    @acoordList.setter
+    def acoordList(self, al):
+        if not isinstance(al, list):
+            raise MxtalError('invalid input atomic structure coordinates, it must be a list')
+
+        for a in al:
+            if not isinstance(a, ACoord):
+                raise MxtalError('invalid data found in atomic structure list')
+
+        self._acoordList = al
+
+    def add(self, symb, c):
+        '''
+        
+        Append an atomc coordinate to existing list
+
+        '''
+        ac = ACoord(symb, c)
+        self._acoordList.append(ac)
+                
+    def __getitem__(self, key):
+
+        '''
+        
+        Array like method for retrieving atomic coordinates
+        
+        '''
+        
+        return self._acoordList[key]
+    
+    def __eq__(self, other):
+        '''
+        
+        Overloading == operator for the atomic coordinates class
+
+        '''
+        import copy
+        if not isinstance(other, Xtal):
+            print("Comparing object of of invalid type")
+            return False  
+        
+        nxtal1 = len(self._acoordList)
+        nxtal2 = len(other.acoordList)
+
+        if nxtal1 != nxtal2:
+            return False
+        
+        if not np.allclose(self._cell, other.cell, atol=1.0e-6):
+            return False
+        
+        clist = copy.deepcopy(self._acoordList)
+        for ac in other.acoordList:
+            if not ac in clist:
+                return False
+            clist.remove(ac)
+
+        return True
+
+    def __repr__(self):
+        '''
+        Present atomic stucture data in .xyz format in standard output. 
+        Refer to `XYZ format <https://wiki.jmol.org/index.php/File_formats/Formats/XYZ>`_
+        for its definition and usage.
+        
+        .. note:: An example of Silicon atomic structure by pyemaps:
+            
+        .. code-block:: console
+
+            216
+                50.0 50.0 50.0 90.0 90.0 90.0
+            SI        	 0.6788375000   0.6788375000   0.6788375000 
+            SI        	 3.3941875000   3.3941875000   0.6788375000 
+            SI        	 4.7518625000   2.0365125000   2.0365125000 
+            SI        	 2.0365125000   4.7518625000   2.0365125000 
+            SI        	 3.3941875000   0.6788375000   3.3941875000 
+            ...
+
+        '''
+        
+        slines = []
+        nxyz = len(self._acoordList)
+        slines.append(str(nxyz))     
+
+        c0, c1, c2, c3, c4, c5 = self._cell
+        slines.append(str(f'\t {c0} {c1} {c2} {c3} {c4} {c5}'))
+
+        for ac in self._acoordList:
+            slines.append(str(ac))
+
+        ret = '\n'.join(slines)
+        return ret   
+
+    def __str__(self):
+        return self.__repr__()

pyemaps-2.0.0.dist-info/METADATA

@@ -0,0 +1,231 @@
+Metadata-Version: 2.4
+Name: pyemaps
+Version: 2.0.0
+Summary: A Python Package for Transmission Electron Diffraction Simulations and Crystallographic Computing
+Home-page: https://www.emlabsolutions.com
+Author: EMLab Solutions, Inc.
+Author-email: support@emlabsoftware.com
+License: Free for base features. License activation required for extended 4dstem features
+Keywords: Transmission,Electron,Diffraction,Simulation,Crystallography,Python
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: license.txt
+License-File: COPYING
+Requires-Dist: emaps>=2.0.0
+Requires-Dist: numpy>=2.0
+Requires-Dist: matplotlib>=3.8.4
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
+
+<!-- #  Open Source __pyEMAPS__ Development Guidelines -->
+
+1. <a id="contents"></a>[What's in pyEMAPS](#overview)
+2. <a id="contents"></a>[Build pyEMAPS](#build)
+3. <a id="contents"></a>[Installation](#installation)
+4. <a id="contents"></a>[Testing](#test)
+5. <a id="contents"></a>[Development Guidelines](#process)
+5. <a id="contents"></a>[pyEMAPS Contributor License Agreement](#CLA)
+5. <a id="contents"></a>[Code of Conduct](#COC)
+
+## What's in pyEMAPS [`↩`](#contents) <a id="overview"></a>
+**pyEMAPS** package is a collection of python modules and libraries designed 
+for transmission electron diffraction simulations and crystallographic calculations 
+for all crystal systems. The simulation is based on the theories of kinematical and 
+dynamical electron diffraction, as described by Spence and Zuo in the book of Electron Microdiffraction (Plenum, New York, 1992).
+
+The base version is free for personal and commercial use, while additional licensed features in 4DSTEM are available for enhanced functionality.
+
+### Features:
+Free base features:
+- Crystallography
+  - Crystal constructor
+  - Loading from a built-in crystal library
+  - CIF import
+  - Crystallographic transformations
+  - Real and reciprocal vector calculations
+  - Stereodiagram plotting
+  - Crystal Structure Factors Calculations
+
+- Electron diffraction pattern, dynamical
+  - Convergent beam electron diffraction
+  - Electron scattering Matrix
+  - Electron dispersion
+
+- Electron diffraction pattern, kinematical
+  - Selected area diffraction
+  - Kikuchi and high order Laue zone line geometry
+  - Convergent beam electron diffraction
+  - Electron powder diffraction simulations
+
+**Extended features** (requires license):
+- Electron diffraction patterns database builder and explore
+- Electron diffraction pattern indexing
+- Annular bright and dark field
+- Masked images 
+
+Check our full [pyemaps documentation](https://emlab-solutions.github.io/pyemaps) for details of __pyEMAPS__ python classes designs and their interfaces.
+
+We are looking for experts in electron microscope and crystallography, and/or python enthusiasts to join pyEMAPS project as contributors, please contact us at support@emlabsoftware.com if you are interested.
+
+We greatly appreciate your contributions to pyEMAPS and look forward to making it a tool for the communty to accelaerate microscopy and crystallography education and research. If you benefit from __pyEMAPS__ in your microscopy and crystallography research and education, go to [PayPal](https://www.paypal.com/paypalme/pyemaps22) to donate. Your generous donations keep us in the business of providing software tools to the education and research communities. 
+
+See instructions below for contributor:
+
+## Build pyEMAPS [`↩`](#content) <a id="build"></a>
+
+Requirements and recommendations:
+* __Python__: Version 3.12, 3.13, 3.14 or 3.15
+* __Operating Systems__: Windows
+* __VSCode__: code editing (recommended, for contributors only)
+
+Building __pyEMAPS__ itself needs no compiler, because it is pure Python. Its compiled backend, __emaps__, supports Windows with Python 3.12 to 3.15, so __pyEMAPS__ does too. pyEMAPS 1.1.x remains available for Python 3.7. We are also looking for contributors to extend it to other platforms. 
+
+Like many python development, a virtual python environment is recommended to isolate your pyEMAPS development environment from your other python development projects.
+
+Below are steps to establish __pyEMAPS__ build environment with python 3.12 as an example:
+
+* Download the Python 3.12 Windows installer (64-bit) from [python.org](https://www.python.org/downloads/windows/).
+* Run the installer, choose the following in installer GUI:
+  
+     * Select Customize Installation
+     * Check and select pip
+     * Install for all users/specific users   
+* Create a virtual environment called "pyemaps_build" for the build
+     * Create a dev directory:
+       ```
+       mkdir pyemaps-dev
+       ``` 
+       (or choose your own directory name)
+     * Create pyemaps_build virtual environemnt:
+       ```
+       py -3.12 -m venv pyemaps_build
+       ```
+* Activate pyemaps_build vitual environment:
+     ```
+    .\pyemaps_build\Scripts\activate
+     ```
+* Update pip:
+  ```
+   python -m pip install pip --upgrade
+  ```
+* Install other python packages required for building pyemaps, using pip:
+  ``` 
+  pip install setuptools wheel build
+  ```
+* Build directory structure:
+
+<pre>
+📦pyemaps
+  ┣━ 📂.git          <----Source repository configurations
+  ┣━ 📂build         <----Intermediate build folder
+  ┣━ 📂dist          <----Build package files
+  ┣━ 📂cdata         <----Built-in crystal data in proprietory format
+  ┣━ 📂CifFile       <----CIF crystal data reader
+  ┣━ 📂diffract      <----Diffraction modules python interfaces
+  ┣━ 📂docs          <----Documentation using Sphinx. Document your changes!
+  ┣━ 📂samples       <----Sample code. Offical sample code for guiding pyemaps usages
+  ┣━ 📂scattering    <----Scattering data module
+  ┣━ 📂spg           <----Space group data module
+  ┗━ 📂test          <----Test cases including sanity, unit and stree tests. Keep adding them!
+</pre>
+where _docs_ for creation of documents requires Sphinx python package:
+- Sphinx for documentation can be installed:
+```
+       pip install Sphinx=5.3.0
+```
+
+* Build pyEMAPS package, run:
+  ```
+   python build_pyemaps -t -v 1.0.0
+  ```
+  Here the option "-t" indicates build is for local testing purposes. 
+  You can replace the version number '1.0.0' with the one you desire.
+
+  When the option _-v_ is not specified. The build script will figure out the version
+  from pypi.org repository.
+
+  Note: there will be two additional diretcories:
+  - _build_.  folder holding intermediate build files.
+  - _dist_. folder for final package that includes .whl and .tgz. The former is the package file and the latter is the current source code used to build the pacage in compressed format. 
+
+## Installation [`↩`](#contents) <a id="installation"></a>
+
+* Install the new pyEMAPS package:
+  ```
+   pip install .\dist\pyemaps-1.0.0-py3-none-any.whl
+  ```
+  This will install new pyEMAPS just built in current python virtual environment
+  along with all of its dependent packages. 
+  
+  If you have a previous _pyemaps_ with versiual or larger than current package version.
+  In that case, you need to uninstall previous version before installing the new package:
+  ```
+  pip uninstall pyemaps
+  ```
+
+## Testing [`↩`](#contents) <a id="test"></a>
+
+  Current pyEMAPS development comes with a set of basic testing suites, including 
+   * sanity checks
+   * unit tests
+   * stress tests.
+
+   To run these test suites, call:
+   ```
+      .\test\sanity\sanity.bat
+   ```
+   We are looking for your tests contributions to make the development to keep high quality standards for _pyEMAPS_.
+
+## Development Guidelines [`↩`](#contents) <a id="process"></a>
+
+As any open source development project, we strongly recommend contributors to adhere to the following guidelines:
+
+* __Issues creation__. Before making changes for bug fix or feature implementation, create an issue in   the pyEMAPS' repository. Your concise description of the issue(s) serves well not only in laying good foundations for your design and implementations, but also in communicating to your fellow contributors.
+
+* __Development Branch__. Create your own branch from 'main' where you work on your changes. The main branch is kept as production base.
+  
+* __Backwards Compatibilities Tests__. Existing test suites designed for testing most of the features are to ensure that no existing implementations are unintentionally broken after new changes are introduced.
+
+* __New Tests Additions__. Writing new test cases for the new implementations are strongly encouraged. 
+  
+* __Pull Requests__. Before merging your changes into production branch "main", a pull request is required. The request should also accompany a list of code reviewers from the contributors. 
+  
+* __Code Review__. We took code review seriously, whether you are reviewing code or your code is being reviewed. This process provides important step of making sound implementations and preventing new bugs.  
+  
+* __Documentation__. You are the author of the new implementations, so please take the pride by documenting them!  
+  We use sphinx tool for documentation generation. To install sphinx, run:
+  ```
+  pip install -U sphinx
+  ```
+  in your python build virtual environment (pyemaps_build in our example).
+
+  Most of the documentations files are in "docs" directory. After making documentation changes to record your changes, compile them with sphinx:
+  ```
+  sphinx-build -b html source .
+  ```
+  The changes resulted from the above can be previewed by opening index.html with avaliable browser.
+  
+## pyEMAPS Contributor License Agreement [`↩`](#contents) <a id="CLA"></a>
+
+Please read and agree to our [Contributor License Agreement](CONTRIBUTING.md) before contributing to this project.
+
+## Code of Conduct [`↩`](#contents) <a id="COC"></a>
+
+pyEMAPS is committed to providing a welcoming and inclusive environment for all contributors. We follow the [Contributor Covenant](https://www.contributor-covenant.org/version/2/0/code_of_conduct/) as our code of conduct. Please make sure to review it before contributing.
+
+**[Read the Contributor Covenant](https://www.contributor-covenant.org/version/2/0/code_of_conduct/)**
+
+Any instances of unacceptable behavior can be reported to support@emlabsoftware.com.
+
+

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